Strain identifier

BacDive ID: 140082

Type strain: Yes

Species: Methyloprofundus sedimenti

Strain Designation: WF1, whale fall 1

Strain history: <- P. Tavormina, California Inst. Technology (Caltech), Pasadena, USA; ATCC BAA-2619

NCBI tax ID(s): 1420851 (species)

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General

@ref: 42689

BacDive-ID: 140082

DSM-Number: 29215

keywords: genome sequence, 16S sequence, Bacteria

description: Methyloprofundus sedimenti WF1 is a bacterium that was isolated from deep sea sediment.

NCBI tax id

  • NCBI tax id: 1420851
  • Matching level: species

strain history

  • @ref: 42689
  • history: <- P. Tavormina, California Inst. Technology (Caltech), Pasadena, USA; ATCC BAA-2619

doi: 10.13145/bacdive140082.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Methylococcales
  • family: Methylococcaceae
  • genus: Methyloprofundus
  • species: Methyloprofundus sedimenti
  • full scientific name: Methyloprofundus sedimenti Tavormina et al. 2015

@ref: 42689

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Methylococcales

family: Methylococcaceae

genus: Methyloprofundus

species: Methyloprofundus sedimenti

full scientific name: Methyloprofundus sedimenti Tavormina et al. 2015

strain designation: WF1, whale fall 1

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 42689
  • name: METHYLOPROFUNDUS SEDIMENTI MEDIUM (DSMZ Medium 1567)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1567
  • composition: Name: METHYLOPROFUNDUS SEDIMENTI MEDIUM (DSMZ Medium 1567) Composition: NaCl 19.8 g/l MgSO4 x 6 H2O 1.0 g/l KNO3 1.0 g/l Na2HPO4 x 12 H2O 0.716 g/l KH2PO4 0.26 g/l MgSO4 x 7 H2O 0.003 g/l Fe(III)-EDTA 0.00152 g/l Nitrilotriacetic acid 0.0015 g/l MnSO4 x H2O 0.0005 g/l ZnSO4 x 7 H2O 0.00018 g/l CoSO4 x 7 H2O 0.00018 g/l CaCl2 x 2 H2O 0.0001 g/l FeSO4 x 7 H2O 0.0001 g/l NiCl2 x 6 H2O 3e-05 g/l AlK(SO4)2 x 12 H2O 2e-05 g/l Pyridoxine hydrochloride 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l H3BO3 1e-05 g/l CuSO4 x 5 H2O 1e-05 g/l Lipoic acid 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l Na2SeO3 x 5 H2O 3e-07 g/l Vitamin B12 1e-07 g/l Distilled water

culture temp

  • @ref: 42689
  • growth: positive
  • type: growth
  • temperature: 20

Isolation, sampling and environmental information

isolation

  • @ref: 42689
  • sample type: deep sea sediment
  • geographic location: Monterey canyon off the coast of California (36.708° N 122.105° W; 1828 m below sea-level)
  • country: USA
  • origin.country: USA
  • continent: North America
  • latitude: 36.708
  • longitude: -122.105

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6524.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_194;96_3091;97_3792;98_4814;99_6524&stattab=map
  • Last taxonomy: Methyloprofundus sedimenti subclade
  • 16S sequence: KF484906
  • Sequence Identity:
  • Total samples: 919
  • soil counts: 96
  • aquatic counts: 805
  • animal counts: 10
  • plant counts: 8

Safety information

risk assessment

  • @ref: 42689
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42689
  • description: Methyloprofundus sedimenti strain WF1 16S ribosomal RNA gene, partial sequence
  • accession: KF484906
  • length: 1414
  • database: nuccore
  • NCBI tax ID: 1420851

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methyloprofundus sedimenti WF1GCA_002072955contigncbi1420851
66792Methyloprofundus sedimenti WF12785510765draftimg1420851

GC content

  • @ref: 42689
  • GC-content: 40.5
  • method: sequence analysis

External links

@ref: 42689

culture collection no.: DSM 29215, ATCC BAA-2619

straininfo link

  • @ref: 96495
  • straininfo: 399606

literature

  • topic: Phylogeny
  • Pubmed-ID: 25342114
  • title: Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs.
  • authors: Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson KS, Connon SA, Orphan VJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.062927-0
  • year: 2014
  • mesh: Bacterial Typing Techniques, Base Composition, California, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Methane/metabolism, Methylococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42689Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29215Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29215)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96495Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399606.1